Bagging regulates the fruit microenvironment and improves the quality and market value of fruits. It is a safe and ecofriendly technique to protect fruits from insect/pest infestation and multiple biotic and abiotic stresses. In the current study, the influence of fruit bagging was evaluated on the development and quality of loquat fruits. Fruits from a healthy loquat orchard (Cv. Zaozhong No.6), located in Fujian, China, were enveloped in paper (T1), aluminum (T2), and aluminum–polyethylene bags (T3), while unbagged fruits were maintained as control (T0). In general, fruit bagging improved fruit quality in terms of fruit physiological and biochemical attributes and protected fruits from physical damage. In particular, aluminum–polyethylene bagging enhanced fruit weight, length, and width by 1.37-, 1.18-, and 1.13-fold, respectively. Loquat fruits bagged with paper bags exhibited the maximum soluble sugar and lowest titratable acid content. Fruits treated with paper and aluminum–ethylene bags showed twofold higher sugar–acid ratio as compared to control. Aluminum–polyethylene bagging caused 66.67%, 55.56%, and 33.33% reductions in skin burn, fruit rotting, and black spot of loquat. The fruits bagged in aluminum and aluminum–polyethylene did not show insect or bird damage, while unbagged fruits had 14.70% and 17.65% insect and bird damage, respectively. Overall, the results suggest that paper, aluminum, and aluminum–polyethylene bagging improved fruit health by 75%, 131%, and 144%, respectively, as compared to control. To delineate bagging type-dependent effects, principal component analysis was performed. Paper bagging was positively correlated with fruit firmness, rotting, soluble sugars, sugar–acid ratio, and proline content. Aluminum bagging was highly associated with improvements in titratable acids, cystine, and methionine. Aluminum–polyethylene bags were correlated with fruit weight, size, peel thickness, edible rate, and certain amino acids.